Developments in coalescent theory from single loci to chromosomes

DOI10.1016/j.tpb.2020.02.002OpenAlexW3009071780WikidataQ90127197 ScholiaQ90127197MaRDI QIDQ2185189

John Wakeley

Publication date: 4 June 2020

Published in: Theoretical Population Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.tpb.2020.02.002

zbMATH Keywords

population geneticsrecombinationgene genealogiescoalescent theorymutation models

Mathematics Subject Classification ID

Biology and other natural sciences (92-XX)

Related Items

Statistical challenges in tracking the evolution of SARS-CoV-2 ⋮ Fifty years of theoretical population biology

Uses Software

• LAMARC
• BEAST
• BEAUti

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• The Moran model with selection: fixation probabilities, ancestral lines, and an alternative particle representation
• Duality, ancestral and diffusion processes in models with selection
• Inference on admixture fractions in a mechanistic model of recurrent admixture
• The ancestral selection graph under strong directional selection
• A sequentially Markov conditional sampling distribution for structured populations with migration and recombination
• Genetic hitchhiking in spatially extended populations
• Line-of-descent and genealogical processes, and their applications in population genetics models
• Lines of descent and the coalescent
• Pólya-like urns and the Ewens' sampling formula
• A note on distributions of times to coalescence, under time-dependent population size
• Approximating selective sweeps
• Non-equilibrium theory of the allele frequency spectrum
• An approximate sampling formula under genetic hitchhiking
• Neutral two-locus multiple allele models with recombination
• Estimation of the neutral mutation rate in a finite population from DNA sequence data
• The use of sample genealogies for studying a selectively neutral m-loci model with recombination
• Partition structures, Polya urns, the Ewens sampling formula, and the ages of alleles
• The infinitely-many-sites model as a measure-valued diffusion
• The sampling theory of neutral alleles and an urn model in population genetics
• The population structure associated with the Ewens sampling formula
• Lines of descent in the diffusion approximation of neutral Wright-Fisher models
• The coalescent
• The effect of strongly selected substitutions on neutral polymorphism: Analytical results based on diffusion theory
• A note on the sampling theory for infinite alleles and infinite sites models
• On the number of segregating sites in genetical models without recombination
• Wandering distributions and the electrophoretic profile
• Reversibility and the age of an allele. I: Moran's infinitely many neutral alleles model
• Is the most frequent allele the oldest?
• A note on multidimensional models of neutral mutation
• Recombination as a point process along sequences
• Simulating probability distributions in the coalescent
• Ancestral processes with selection
• A Markov chain model of coalescence with recombination
• The asymptotic behavior of an urn model arising
• Mathematical population genetics. I: Theoretical introduction.
• Logarithmic combinatorial structures: A probabilistic approach
• The probability of topological concordance of gene trees and species trees.
• Simulation of selected genealogies.
• Most recent common ancestor probability distributions in gene genealogies under selection.
• Coalescents with multiple collisions
• Conditional genealogies and the age of a neutral mutant
• The ancestral graph and gene genealogy under frequency-dependent selection
• Coalescents with simultaneous multiple collisions
• Ancestral inference in population genetics
• Full likelihood inference from the site frequency spectrum based on the optimal tree resolution
• Population structure and coalescence in pedigrees: comparisons to the structured coalescent and a framework for inference
• General theory for stochastic admixture graphs and \(F\)-statistics
• Forward and backward diffusion approximations for haploid exchangeable population models.
• Alpha-stable branching and beta-coalescents
• Particle representations for measure-valued population models
• Properties of a neutral allele model with intragenic recombination
• A classification of coalescent processes for haploid exchangeable population models
• Coalescence in a random background.
• Statistical properties of segregating sites
• Rate matrix estimation from site frequency data
• An analytical framework in the general coalescent tree setting for analyzing polymorphisms created by two mutations
• Genealogical constructions of population models
• The probability of reciprocal monophyly of gene lineages in three and four species
• Finding the best resolution for the Kingman-Tajima coalescent: theory and applications
• The neutral frequency spectrum of linked sites
• Theoretical foundation of population genetics at the molecular level
• The rate of loss of multiple alleles in finite haploid populations
• The sampling theory of selectively neutral alleles
• Addendum to a paper of W. Ewens
• A countable representation of the Fleming-Viot measure-valued diffusion
• Looking down in the ancestral selection graph: a probabilistic approach to the common ancestor type distribution
• Recent progress in coalescent theory
• Probability Models for DNA Sequence Evolution
• The stationary distribution of the infinitely-many neutral alleles diffusion model
• Coherent random walks arising in some genetical models
• Exact sampling distributions from the infinite neutral alleles model
• Robustness results for the coalescent
• The age of a mutation in a general coalescent tree
• Inference in Molecular Population Genetics
• The sampling theory of selectively neutral alleles
• The general coalescent with asynchronous mergers of ancestral lines
• Times on trees, and the age of an allele